The weakness of this system of mandate-and-waiver is its lack of legitimacy. If the public's attention can be focused on HHS bureaucrats denying particular insurance policies to particular people, then the Obama administration will be forced to choose between backing off or getting mired in a losing public relations fight.
Since the Obama administration is certain to make use of the strengths of the mandate-and-waiver to advance the cause of government-run health care, conservative politicians should use the political weaknesses of this approach (and the potential policy space this weakness opens up) not only to weaken Obamacare but to increase the numbers of Americans with consumer-driven health insurance policies. Republican gains in governorships and state legislature seats gives the GOP an opportunity to force supporters of government-run health care to either retreat or fight (hopefully) losing political battles.

The states can help:

One way that Republican governors and state legislators can weaken Obamacare is to reform their Medicaid systems into a subsidy for high deductible private insurance coverage. A second way is for GOP governors and state legislators to adopt and expand Mitch Daniels' policy of offering and HSA/catastrophic insurance coverage to Indiana state employees. This approach has saved Indiana money (which is pretty important considering the circumstances of many state budgets) and increased the take home pay of Indiana state employees while expanding the number of Americans with consumer-driven health care policies in a consensual (rather than mandated) way. Other states should adopt this approach for their own state workers and make it mandatory that municipal governments offer identical HSA/catastrophic coverage plans to municipal workers as union contracts expire. Let the union leadership fight not only the taxpayers, but their own members who might want the option of picking HSA/catastrophic insurance plans that would save them money in premium costs. Also, let HHS and the Obama administration explain why a plan that is good enough for Indiana's employees isn't good enough for Kansas, Florida, or Georgia. And let Republicans in Congress push for laws giving states the unambiguous legal authority to enact these kinds of policies.
This approach of reforming Medicaid in a free market direction and giving an HSA/catastrophic coverage option to state and municipal employees has the potential to sharply increase the number of Americans in consumer-driven policies, making it much more politically difficult for the Democrats to abolish these kinds of plans through either legislation or bureaucratic fiat. It also gives conservatives arguments in favor of eventually expanding use of these kinds of insurance policies to groups other than Medicaid clients and public employees. If they are good enough for those two groups, they are good enough for most of the rest of the working public. The very act of fighting the Obama administration for waivers for these kinds of policies will tend to increase public awareness of the existence and benefits of free market-oriented health care reform policies.